SMTL ID : 7edd.1

Crystal structure of a serine protease from Streptococcus pyogenes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: H.185, S.252, N.287, T.522, S.523 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.287, A:N.287, A:S.523, A:S.523 Salt bridges: A:H.185 SO4.2: 1 residues within 4Å: Chain A: R.1079 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.1079 SO4.3: 3 residues within 4Å: Chain A: F.823, L.879, A.882 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.879

10 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.5: 6 residues within 4Å: Chain A: K.956, S.958, F.989, M.1013, E.1015 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.1015 CA.6: 5 residues within 4Å: Chain A: D.923, Q.925, D.948, R.949, D.1016 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.923, A:Q.925, A:D.948, A:R.949, A:D.1016 CA.7: 5 residues within 4Å: Chain A: S.814, N.816, D.818, N.820, D.822 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.814, A:S.814, A:D.818, A:N.820, A:D.822 CA.8: 1 residues within 4Å: Chain A: N.820 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain A: E.1443, P.1468 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.1443 CA.10: 3 residues within 4Å: Chain A: Q.725, E.727, Y.1432 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.727 CA.11: 4 residues within 4Å: Chain A: S.127, F.207, T.510, Y.516 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.127, A:Y.516 CA.12: 6 residues within 4Å: Chain A: S.1096, N.1098, D.1100, N.1102, D.1104, G.1287 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.1096, A:S.1096, A:D.1100, A:N.1102, A:D.1104 CA.22: 3 residues within 4Å: Chain A: G.910, H.1404 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.1404, A:H.1404

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: E.773, T.774, K.987, M.1013, E.1015, V.1021 Ligands: CA.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.774, A:T.774, A:K.987, A:E.1015 GOL.14: 10 residues within 4Å: Chain A: S.772, E.773, T.774, N.775, T.780, D.818, N.820, Y.1048, Q.1049, T.1050 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.772, A:S.772, A:N.775, A:T.780, A:Y.1048, A:Q.1049 GOL.15: 12 residues within 4Å: Chain A: Q.835, Y.905, P.906, V.908, V.909, G.910, A.911, Q.1400, T.1402, V.1471, E.1473 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.835, A:G.910, A:Q.1400, A:T.1402, A:E.1473 GOL.16: 9 residues within 4Å: Chain A: Q.260, R.315, Y.495, L.496, D.602, Y.604, S.606, I.607, S.608 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.260, A:R.315, A:L.496, A:L.496, A:D.602 GOL.17: 7 residues within 4Å: Chain A: M.1195, I.1196, T.1197, K.1214, T.1215, K.1216, I.1223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.1197, A:K.1216

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.18: 2 residues within 4Å: Ligands: CL.20, CL.21 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.19: 8 residues within 4Å: Chain A: A.730, V.731, A.732, E.734, Y.904, Q.914, E.915, M.916 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.731, A:A.732, A:E.734, A:Q.914

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 2 residues within 4Å: Ligands: MG.18, CL.21 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Ligands: MG.18, CL.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jobichen, C. et al., The Autocatalytic Cleavage Domain Is Not Required for the Activity of ScpC, a Virulence Protease from Streptococcus pyogenes : A Structural Insight. Biochemistry (2021)

Release Date

2021-05-12

Peptides

C5a peptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C5a peptidase